cd-hit →
4.6.1-2012-08-27-2 →
armhf → 2013-08-26 12:48:00
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testbuildd.raspbian.org
╔══════════════════════════════════════════════════════════════════════════════╗
║ cd-hit 4.6.1-2012-08-27-2 (armhf) 26 Aug 2013 12:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: cd-hit
Version: 4.6.1-2012-08-27-2
Source Version: 4.6.1-2012-08-27-2
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/cd-hit-W0cL2U/cd-hit-4.6.1-2012-08-27' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/cd-hit-W0cL2U' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-863f21a4-067d-421d-bf93-95e87cc561e9' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging Release.gpg [490 B]
Get:2 http://172.17.0.1 jessie-staging Release [10.8 kB]
Get:3 http://172.17.0.1 jessie-staging/main Sources [6779 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7931 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 14.7 MB in 1min 53s (129 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'cd-hit' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/cd-hit/trunk/
Need to get 660 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main cd-hit 4.6.1-2012-08-27-2 (dsc) [1411 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main cd-hit 4.6.1-2012-08-27-2 (tar) [652 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main cd-hit 4.6.1-2012-08-27-2 (diff) [5710 B]
Fetched 660 kB in 2s (274 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-CEJQHD/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 52 not upgraded.
Need to get 0 B/704 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11338 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man
dpkg-deb: building package `sbuild-build-depends-cd-hit-dummy' in `/«BUILDDIR»/resolver-KwuZts/apt_archive/sbuild-build-depends-cd-hit-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install cd-hit build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-cd-hit-dummy
0 upgraded, 19 newly installed, 0 to remove and 52 not upgraded.
Need to get 8486 kB/8487 kB of archives.
After this operation, 22.5 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.4-1 [36.9 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.5-2 [949 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3-1 [29.4 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.4-1 [1907 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3-1 [136 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3-1 [1837 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20130630 [710 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.43.3 [104 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8486 kB in 60s (140 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11338 files and directories currently installed.)
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.4-1_armhf.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.22.2-3_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_armhf.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.5-2_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.3-1_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package libxml2:armhf.
Unpacking libxml2:armhf (from .../libxml2_2.9.1+dfsg1-3_armhf.deb) ...
Selecting previously unselected package libffi6:armhf.
Unpacking libffi6:armhf (from .../libffi6_3.0.13-4_armhf.deb) ...
Selecting previously unselected package libglib2.0-0:armhf.
Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.36.4-1_armhf.deb) ...
Selecting previously unselected package libcroco3:armhf.
Unpacking libcroco3:armhf (from .../libcroco3_0.6.8-2_armhf.deb) ...
Selecting previously unselected package libunistring0:armhf.
Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.3-1_armhf.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.3-1_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
Unpacking debhelper (from .../debhelper_9.20130630_all.deb) ...
Selecting previously unselected package help2man.
Unpacking help2man (from .../help2man_1.43.3_armhf.deb) ...
Selecting previously unselected package sbuild-build-depends-cd-hit-dummy.
Unpacking sbuild-build-depends-cd-hit-dummy (from .../sbuild-build-depends-cd-hit-dummy.deb) ...
Setting up libpipeline1:armhf (1.2.4-1) ...
Setting up groff-base (1.22.2-3) ...
Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3-1) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglib2.0-0:armhf (2.36.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.3-1) ...
Setting up gettext (0.18.3-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20130630) ...
Setting up help2man (1.43.3) ...
Setting up sbuild-build-depends-cd-hit-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.9.8-imx5 armhf (armv7l)
Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.4-2+rpi1 gcc-4.6_4.6.4-2+rpi1 libc6-dev_2.17-3 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: apt_0.9.7.8+rpi1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.22-8 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.4 build-essential_11.6 bzip2_1.0.6-4 coreutils_8.13-3.5 cpio_2.11+dfsg-1 cpp_4:4.6.3-8 cpp-4.6_4.6.4-2+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130630 debianutils_4.3.4 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.4-2+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-2+rpi1 gcc-4.6-base_4.6.4-2+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8-base_4.8.0-7+rpi1 gettext_0.18.3-1 gettext-base_0.18.3-1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.5-1.1 help2man_1.43.3 hostname_3.12 initramfs-tools_0.112 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.7.8+rpi1 libasprintf0c2_0.18.3-1 libattr1_1:2.4.47-1 libblkid1_2.20.1-5.4 libbz2-1.0_1.0.6-4 libc-bin_2.17-3 libc-dev-bin_2.17-3 libc6_2.17-3 libc6-dev_2.17-3 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-5 libdbus-1-3_1.6.10-1 libdpkg-perl_1.16.10 libffi6_3.0.13-4 libgc1c2_1:7.1-9.1 libgcc1_1:4.8.0-7+rpi1 libgdbm3_1.8.3-12 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.2+dfsg-1 libgomp1_4.8.0-7+rpi1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.4 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130504-1 libncursesw5_5.9+20130504-1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libprocps0_1:3.3.4-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130504-1 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.4 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.4 multiarch-support_2.17-3 ncurses-base_5.9+20130504-1 ncurses-bin_5.9+20130504-1 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 plymouth_0.8.8-6 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-cd-hit-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.7 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-6 tzdata_2013c-2 udev_175-7.2 util-linux_2.20.1-5.4 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Aug 15 19:40:24 2013 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./cd-hit_4.6.1-2012-08-27-2.dsc
dpkg-source: info: extracting cd-hit in cd-hit-4.6.1-2012-08-27
dpkg-source: info: unpacking cd-hit_4.6.1-2012-08-27.orig.tar.gz
dpkg-source: info: unpacking cd-hit_4.6.1-2012-08-27-2.debian.tar.gz
dpkg-source: info: applying enable_help2man.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-863f21a4-067d-421d-bf93-95e87cc561e9
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
previous=N
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package cd-hit
dpkg-buildpackage: source version 4.6.1-2012-08-27-2
dpkg-source --before-build cd-hit-4.6.1-2012-08-27
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
rm -f *.o cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_auto_build -- openmp=yes
make[2]: Entering directory `/«PKGBUILDDIR»'
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-common.c++ -c
cdhit-common.c++: In member function 'void SequenceDB::DoClustering(const Options&)':
cdhit-common.c++:2994:66: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t {aka unsigned int}' [-Wformat]
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-utility.c++ -c
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit.c++ -c
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-est.c++ -c
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-est.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-est
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-2d.c++ -c
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-2d
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-est-2d.c++ -c
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-est-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-est-2d
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-div.c++ -c
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-div.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-div
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-454.c++ -c
g++ -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security cdhit-454.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -o cd-hit-454
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_auto_install -- PREFIX=debian/cd-hit/usr/lib/cd-hit
make[2]: Entering directory `/«PKGBUILDDIR»'
for prog in cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454; do \
install -m 0755 $prog debian/cd-hit/usr/lib/cd-hit; \
done
install -m 0755 *.pl debian/cd-hit/usr/lib/cd-hit;
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory `/«PKGBUILDDIR»'
mkdir -p /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1/
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='quickly group sequences' \
/«PKGBUILDDIR»/cd-hit | \
sed -e 's/^cd-\(hit \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \
> /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit.1
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='quickly group sequences, optimised for 454 data' \
/«PKGBUILDDIR»/cd-hit-454 | \
sed -e 's/^cd-\(hit \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \
> /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit-454.1
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='quickly group sequences in db1 or db2 format' \
/«PKGBUILDDIR»/cd-hit-2d | \
sed -e 's/^cd-\(hit-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \
> /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit-2d.1
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='run CD-HIT algorithm on RNA/DNA sequences' \
/«PKGBUILDDIR»/cd-hit-est | \
sed -e 's/^cd-\(hit-est \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \
> /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit-est.1
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format' \
/«PKGBUILDDIR»/cd-hit-est-2d | \
sed -e 's/^cd-\(hit-est-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \
> /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cdhit-est-2d.1
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs' \
/«PKGBUILDDIR»/cd-hit-2d-para.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cd-hit-2d-para.1
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs' \
/«PKGBUILDDIR»/cd-hit-para.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//cd-hit-para.1
# psi-cd-hit.pl is throwing some errors which are fixed using sed
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities' \
/«PKGBUILDDIR»/psi-cd-hit.pl | \
sed -e '/^Name "main::.*" used only once:/d' \
> /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//psi-cd-hit.1
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \
/«PKGBUILDDIR»/psi-cd-hit-2d.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d.1
# FIXME: what is the difference between psi-cd-hit-2d.pl and psi-cd-hit-2d-g1.pl ?
help2man --no-info --no-discard-stderr --version-string='4.6.1-2012-08-27' \
--name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \
/«PKGBUILDDIR»/psi-cd-hit-2d-g1.pl > /«PKGBUILDDIR»/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d-g1.1
# No help output from
# cd-hit-div.pl
# clstr2tree.pl
# clstr_merge.pl
# clstr_merge_noorder.pl
# clstr_reduce.pl
# clstr_renumber.pl
# clstr_rev.pl
# clstr_sort_by.pl
# clstr_sort_prot_by
# make_multi_seq
# psi-cd-hit-local.pl -> even throws several "used only once: possible typo" errors
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_perl -a
dh_link -a
debian/rules override_dh_compress
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_compress --exclude=.pdf
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `cd-hit' in `../cd-hit_4.6.1-2012-08-27-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../cd-hit_4.6.1-2012-08-27-2_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build cd-hit-4.6.1-2012-08-27
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130826-1247
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
cd-hit_4.6.1-2012-08-27-2_armhf.changes:
────────────────────────────────────────
Format: 1.8
Date: Thu, 15 Aug 2013 21:36:49 +0200
Source: cd-hit
Binary: cd-hit
Architecture: armhf
Version: 4.6.1-2012-08-27-2
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
cd-hit - suite of programs designed to quickly group sequences
Changes:
cd-hit (4.6.1-2012-08-27-2) unstable; urgency=low
.
* Take over changes from BioLinux
Checksums-Sha1:
7e9f4914c4c972b4e78c2c825b52433740c9751e 686086 cd-hit_4.6.1-2012-08-27-2_armhf.deb
Checksums-Sha256:
43c75cd5460af04accd7a3a401d6d01e77efef2a54cc51025d9310719b39b8b6 686086 cd-hit_4.6.1-2012-08-27-2_armhf.deb
Files:
320d2d0c99a203663f35dbb78af4db95 686086 science optional cd-hit_4.6.1-2012-08-27-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
cd-hit_4.6.1-2012-08-27-2_armhf.deb
───────────────────────────────────
new debian package, version 2.0.
size 686086 bytes: control archive=2152 bytes.
911 bytes, 17 lines control
3529 bytes, 53 lines md5sums
Package: cd-hit
Version: 4.6.1-2012-08-27-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1134
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.4.0), perl
Section: science
Priority: optional
Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
Description: suite of programs designed to quickly group sequences
cd-hit contains a number of programs designed to quickly group
sequences. cd-hit groups proteins into clusters that meet a user-defined
similarity threshold. cd-hit-est is similar to cd-hit, but designed to
group nucleotide sequences (without introns). cd-hit-est-2d is similar
to cd-hit-2d but designed to compare two nucleotide datasets. A number
of other related programs are also in this package. Please see the
cd-hit user manual, also part of this package, for further information.
drwxr-xr-x root/root 0 2013-08-26 12:47 ./
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/lib/
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/lib/cd-hit/
-rwxr-xr-x root/root 12596 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-2d-para.pl
-rwxr-xr-x root/root 877 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-div.pl
-rwxr-xr-x root/root 11859 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-para.pl
-rwxr-xr-x root/root 952 2013-08-26 12:47 ./usr/lib/cd-hit/clstr2tree.pl
-rwxr-xr-x root/root 1209 2013-08-26 12:47 ./usr/lib/cd-hit/clstr2txt.pl
-rwxr-xr-x root/root 4503 2013-08-26 12:47 ./usr/lib/cd-hit/clstr2xml.pl
-rwxr-xr-x root/root 464 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_cut.pl
-rwxr-xr-x root/root 3199 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_merge.pl
-rwxr-xr-x root/root 2162 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_merge_noorder.pl
-rwxr-xr-x root/root 3465 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_quality_eval.pl
-rwxr-xr-x root/root 2335 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_quality_eval_by_link.pl
-rwxr-xr-x root/root 1000 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_reduce.pl
-rwxr-xr-x root/root 196 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_renumber.pl
-rwxr-xr-x root/root 554 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_rep.pl
-rwxr-xr-x root/root 1160 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_reps_faa_rev.pl
-rwxr-xr-x root/root 1620 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_rev.pl
-rwxr-xr-x root/root 387 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_select.pl
-rwxr-xr-x root/root 555 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_select_rep.pl
-rwxr-xr-x root/root 779 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_size_histogram.pl
-rwxr-xr-x root/root 725 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_size_stat.pl
-rwxr-xr-x root/root 806 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_sort_by.pl
-rwxr-xr-x root/root 1291 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_sort_prot_by.pl
-rwxr-xr-x root/root 2928 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_sql_tbl.pl
-rwxr-xr-x root/root 1103 2013-08-26 12:47 ./usr/lib/cd-hit/clstr_sql_tbl_sort.pl
-rwxr-xr-x root/root 1670 2013-08-26 12:47 ./usr/lib/cd-hit/make_multi_seq.pl
-rwxr-xr-x root/root 3668 2013-08-26 12:47 ./usr/lib/cd-hit/plot_2d.pl
-rwxr-xr-x root/root 2190 2013-08-26 12:47 ./usr/lib/cd-hit/plot_len1.pl
-rwxr-xr-x root/root 1529 2013-08-26 12:47 ./usr/lib/cd-hit/psi-cd-hit-2d-g1.pl
-rwxr-xr-x root/root 2582 2013-08-26 12:47 ./usr/lib/cd-hit/psi-cd-hit-2d.pl
-rwxr-xr-x root/root 57183 2013-08-26 12:47 ./usr/lib/cd-hit/psi-cd-hit-local.pl
-rwxr-xr-x root/root 2397 2013-08-26 12:47 ./usr/lib/cd-hit/psi-cd-hit.pl
-rwxr-xr-x root/root 107928 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit
-rwxr-xr-x root/root 107928 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-est
-rwxr-xr-x root/root 107928 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-2d
-rwxr-xr-x root/root 107928 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-est-2d
-rwxr-xr-x root/root 107924 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-div
-rwxr-xr-x root/root 108012 2013-08-26 12:47 ./usr/lib/cd-hit/cd-hit-454
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/share/
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/share/doc/cd-hit/
-rw-r--r-- root/root 362533 2012-08-27 21:09 ./usr/share/doc/cd-hit/cdhit-user-guide.pdf
-rw-r--r-- root/root 303 2012-04-26 06:50 ./usr/share/doc/cd-hit/README.Debian
-rw-r--r-- root/root 1982 2012-04-22 07:31 ./usr/share/doc/cd-hit/copyright
-rw-r--r-- root/root 1259 2013-08-15 19:38 ./usr/share/doc/cd-hit/changelog.Debian.gz
-rw-r--r-- root/root 962 2012-08-27 21:09 ./usr/share/doc/cd-hit/changelog.gz
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/share/doc-base/
-rw-r--r-- root/root 753 2011-12-22 08:06 ./usr/share/doc-base/cd-hit
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/share/man/
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/share/man/man1/
-rw-r--r-- root/root 1665 2013-08-26 12:47 ./usr/share/man/man1/cdhit.1.gz
-rw-r--r-- root/root 1360 2013-08-26 12:47 ./usr/share/man/man1/cdhit-454.1.gz
-rw-r--r-- root/root 1696 2013-08-26 12:47 ./usr/share/man/man1/cdhit-2d.1.gz
-rw-r--r-- root/root 1822 2013-08-26 12:47 ./usr/share/man/man1/cdhit-est.1.gz
-rw-r--r-- root/root 1926 2013-08-26 12:47 ./usr/share/man/man1/cdhit-est-2d.1.gz
-rw-r--r-- root/root 1153 2013-08-26 12:47 ./usr/share/man/man1/cd-hit-2d-para.1.gz
-rw-r--r-- root/root 1117 2013-08-26 12:47 ./usr/share/man/man1/cd-hit-para.1.gz
-rw-r--r-- root/root 1597 2013-08-26 12:47 ./usr/share/man/man1/psi-cd-hit.1.gz
-rw-r--r-- root/root 1697 2013-08-26 12:47 ./usr/share/man/man1/psi-cd-hit-2d.1.gz
-rw-r--r-- root/root 343 2013-08-26 12:47 ./usr/share/man/man1/psi-cd-hit-2d-g1.1.gz
drwxr-xr-x root/root 0 2013-08-26 12:47 ./usr/bin/
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/psi-cd-hit -> ../lib/cd-hit/psi-cd-hit.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/psi-cd-hit-local -> ../lib/cd-hit/psi-cd-hit-local.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/psi-cd-hit-2d -> ../lib/cd-hit/psi-cd-hit-2d.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/psi-cd-hit-2d-g1 -> ../lib/cd-hit/psi-cd-hit-2d-g1.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/make_multi_seq -> ../lib/cd-hit/make_multi_seq.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr_sort_prot_by -> ../lib/cd-hit/clstr_sort_prot_by.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr_sort_by -> ../lib/cd-hit/clstr_sort_by.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr_rev -> ../lib/cd-hit/clstr_rev.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr_renumber -> ../lib/cd-hit/clstr_renumber.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr_reduce -> ../lib/cd-hit/clstr_reduce.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr_merge -> ../lib/cd-hit/clstr_merge.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr_merge_noorder -> ../lib/cd-hit/clstr_merge_noorder.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/clstr2tree -> ../lib/cd-hit/clstr2tree.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cd-hit-para -> ../lib/cd-hit/cd-hit-para.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cdhit-est-2d -> ../lib/cd-hit/cd-hit-est-2d
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cdhit-est -> ../lib/cd-hit/cd-hit-est
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cd-hit-div -> ../lib/cd-hit/cd-hit-div.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cdhit-454 -> ../lib/cd-hit/cd-hit-454
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cd-hit-2d-para -> ../lib/cd-hit/cd-hit-2d-para.pl
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cdhit-2d -> ../lib/cd-hit/cd-hit-2d
lrwxrwxrwx root/root 0 2013-08-26 12:47 ./usr/bin/cdhit -> ../lib/cd-hit/cd-hit
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 9984
Build-Time: 135
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 163
Job: cd-hit_4.6.1-2012-08-27-2
Machine Architecture: armhf
Package: cd-hit
Package-Time: 434
Source-Version: 4.6.1-2012-08-27-2
Space: 9984
Status: successful
Version: 4.6.1-2012-08-27-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20130826-1247
Build needed 00:07:14, 9984k disc space